Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7XSE

RNA polymerase II elongation complex transcribing a nucleosome (EC42)

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A	DNA-directed RNA polymerase subunit	polymer	1743	194107.4	1	UniProt (C4R4Y0) Pfam (PF04997) Pfam (PF05001) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) In PDB	Komagataella phaffii
2	B	DNA-directed RNA polymerase subunit beta	polymer	1227	139746.1	1	UniProt (C4QZQ7) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) In PDB	Komagataella phaffii
3	C	RNA polymerase II third largest subunit B44, part of central core	polymer	304	34216.3	1	UniProt (C4R7L2) Pfam (PF01193) Pfam (PF01000) In PDB	Komagataella phaffii
4	D	RNA polymerase II subunit B32	polymer	186	20623.0	1	UniProt (C4R2U9) Pfam (PF03874) In PDB	Komagataella phaffii
5	E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	polymer	214	24962.7	1	UniProt (C4R3P8) Pfam (PF03871) Pfam (PF01191) In PDB	Komagataella phaffii
6	F	RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III	polymer	155	17803.6	1	UniProt (C4R1V1) Pfam (PF01192) In PDB	Komagataella phaffii
7	G	RNA polymerase II subunit	polymer	171	18802.6	1	UniProt (C4R9A1) Pfam (PF03876) Pfam (PF00575) In PDB	Komagataella phaffii
8	H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	polymer	145	16249.2	1	UniProt (C4R273) Pfam (PF03870) In PDB	Komagataella phaffii
9	I	DNA-directed RNA polymerase subunit	polymer	115	13612.3	1	UniProt (F2QPE6) Pfam (PF02150) Pfam (PF01096) In PDB	Komagataella phaffii
10	J	RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III	polymer	72	8554.1	1	UniProt (C4R009) Pfam (PF01194) In PDB	Komagataella phaffii
11	K	RNA polymerase II subunit B12.5	polymer	118	13832.9	1	UniProt (C4R3Z5) Pfam (PF13656) In PDB	Komagataella phaffii
12	L	RNA polymerase subunit ABC10-alpha	polymer	72	7862.0	1	UniProt (F2QMI1) Pfam (PF03604) In PDB	Komagataella phaffii
13	M	Transcription elongation factor 1 homolog	polymer	113	12606.9	1	UniProt (C4QZ45) Pfam (PF05129) In PDB	Komagataella phaffii
14	N	DNA (198-MER)	polymer	198	61381.9	1		synthetic construct
15	P	RNA (5'-R(PUPGPCPCPUPGPGPUPGPUPCPUPUPGPGPGPUPGP*U)-3')	polymer	19	6081.6	1		synthetic construct
16	T	DNA (198-MER)	polymer	198	60870.0	1		synthetic construct
17	V	Transcription elongation factor SPT4	polymer	108	12039.6	1	UniProt (C4R0E6) Pfam (PF06093) In PDB	Komagataella phaffii
18	W	Transcription elongation factor SPT5	polymer	911	101459.4	1	UniProt (C4R370) Pfam (PF11942) Pfam (PF03439) Pfam (PF00467) Pfam (PF12815) In PDB	Komagataella phaffii	Chromatin Elongation factor SPT5,Transcription elongation factor spt5
19	a, e	Histone H3.3	polymer	139	15643.3	2	UniProt (P84243) Pfam (PF00125) In PDB	Homo sapiens (human)
20	b, f	Histone H4	polymer	106	11676.7	2	UniProt (P62805) Pfam (PF15511) In PDB	Homo sapiens (human)
21	c, g	Histone H2A type 1-B/E	polymer	133	14447.8	2	UniProt (P04908) Pfam (PF00125) Pfam (PF16211) In PDB	Homo sapiens (human)	Histone H2A.2,Histone H2A/a,Histone H2A/m
22	d, h	Histone H2B type 1-J	polymer	129	14217.5	2	UniProt (P06899) Pfam (PF00125) In PDB	Homo sapiens (human)	Histone H2B.1,Histone H2B.r,H2B/r
23	m	Transcription elongation factor Spt6	polymer	1503	173241.6	1	UniProt (C4R7H2) Pfam (PF14632) Pfam (PF14641) Pfam (PF22706) Pfam (PF14639) Pfam (PF14635) Pfam (PF21710) Pfam (PF14633) In PDB	Komagataella phaffii
24	n	Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II	polymer	417	46907.8	1	UniProt (C4R7L8) Pfam (PF08711) In PDB	Komagataella phaffii
25	q	Component of the Paf1p complex	polymer	1084	124979.0	1	UniProt (C4R6B2) Pfam (PF13432) In PDB	Komagataella phaffii
26	r	RNAPII-associated chromatin remodeling Paf1 complex subunit	polymer	544	62301.2	1	UniProt (F2QQ42) Pfam (PF03126) In PDB	Komagataella phaffii
27	u	Leo1	polymer	459	52387.7	1	UniProt (C4R3K1) Pfam (PF04004) In PDB	Komagataella phaffii
28	v	RNAP II-associated protein	polymer	396	46046.0	1	UniProt (C4R997) Pfam (PF03985) In PDB	Komagataella phaffii
29	x	Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p	polymer	395	44760.7	1	UniProt (C4R1E6) Pfam (PF05179) In PDB	Komagataella phaffii
30	A, B, C, I, J...	ZINC ION	non-polymer		65.4	10	Chemie (ZN)
31	A	MAGNESIUM ION	non-polymer		24.3	1	Chemie (MG)

Sequence modifications

M: 1 - 110 (UniProt: C4QZ45)

PDB	External Database	Details
Gly -2	-	expression tag
Pro -1	-	expression tag
Gly 0	-	expression tag

V: 8 - 114 (UniProt: C4R0E6)

PDB	External Database	Details
Met 7	-	initiating methionine

W: 1 - 908 (UniProt: C4R370)

PDB	External Database	Details
Gly -2	-	expression tag
Pro -1	-	expression tag
Gly 0	-	expression tag

a, e: 0 - 135 (UniProt: P84243)

PDB	External Database	Details
Gly -3	-	expression tag
Ser -2	-	expression tag
His -1	-	expression tag

b, f: 0 - 102 (UniProt: P62805)

PDB	External Database	Details
Gly -3	-	expression tag
Ser -2	-	expression tag
His -1	-	expression tag

c, g: 0 - 129 (UniProt: P04908)

PDB	External Database	Details
Gly -3	-	expression tag
Ser -2	-	expression tag
His -1	-	expression tag

d, h: -3 - 122 (UniProt: P06899)

PDB	External Database	Details
Gly -6	-	expression tag
Ser -5	-	expression tag
His -4	-	expression tag

m: 1 - 1500 (UniProt: C4R7H2)

PDB	External Database	Details
Gly -2	-	expression tag
Pro -1	-	expression tag
Gly 0	-	expression tag

n: 1 - 414 (UniProt: C4R7L8)

PDB	External Database	Details
Gly -2	-	expression tag
Pro -1	-	expression tag
Gly 0	-	expression tag

q: 1 - 1044 (UniProt: C4R6B2)

PDB	External Database	Details
Met -39	-	initiating methionine
Lys -38	-	expression tag
Asp -37	-	expression tag
His -36	-	expression tag
Leu -35	-	expression tag
Ile -34	-	expression tag
His -33	-	expression tag
Asn -32	-	expression tag
His -31	-	expression tag
His -30	-	expression tag
Lys -29	-	expression tag
His -28	-	expression tag
Glu -27	-	expression tag
His -26	-	expression tag
Ala -25	-	expression tag
His -24	-	expression tag
Ala -23	-	expression tag
Glu -22	-	expression tag
His -21	-	expression tag
Asp -20	-	expression tag
Tyr -19	-	expression tag
Lys -18	-	expression tag
Asp -17	-	expression tag
Asp -16	-	expression tag
Asp -15	-	expression tag
Asp -14	-	expression tag
Lys -13	-	expression tag
Glu -12	-	expression tag
His -11	-	expression tag
Leu -10	-	expression tag
Tyr -9	-	expression tag
Phe -8	-	expression tag
Gln -7	-	expression tag
Gly -6	-	expression tag
Ser -5	-	expression tag
Ser -4	-	expression tag
Gly -3	-	expression tag
Ser -2	-	expression tag
Ser -1	-	expression tag
Gly 0	-	expression tag

r: 1 - 514 (UniProt: F2QQ42)

PDB	External Database	Details
Met -29	-	initiating methionine
Lys -28	-	expression tag
Asp -27	-	expression tag
His -26	-	expression tag
Leu -25	-	expression tag
Ile -24	-	expression tag
His -23	-	expression tag
Asn -22	-	expression tag
His -21	-	expression tag
His -20	-	expression tag
Lys -19	-	expression tag
His -18	-	expression tag
Glu -17	-	expression tag
His -16	-	expression tag
Ala -15	-	expression tag
His -14	-	expression tag
Ala -13	-	expression tag
Glu -12	-	expression tag
His -11	-	expression tag
Leu -10	-	expression tag
Tyr -9	-	expression tag
Phe -8	-	expression tag
Gln -7	-	expression tag
Gly -6	-	expression tag
Ser -5	-	expression tag
Ser -4	-	expression tag
Gly -3	-	expression tag
Ser -2	-	expression tag
Ser -1	-	expression tag
Gly 0	-	expression tag

u: 1 - 429 (UniProt: C4R3K1)

PDB	External Database	Details
Met -29	-	initiating methionine
Lys -28	-	expression tag
Asp -27	-	expression tag
His -26	-	expression tag
Leu -25	-	expression tag
Ile -24	-	expression tag
His -23	-	expression tag
Asn -22	-	expression tag
His -21	-	expression tag
His -20	-	expression tag
Lys -19	-	expression tag
His -18	-	expression tag
Glu -17	-	expression tag
His -16	-	expression tag
Ala -15	-	expression tag
His -14	-	expression tag
Ala -13	-	expression tag
Glu -12	-	expression tag
His -11	-	expression tag
Leu -10	-	expression tag
Tyr -9	-	expression tag
Phe -8	-	expression tag
Gln -7	-	expression tag
Gly -6	-	expression tag
Ser -5	-	expression tag
Ser -4	-	expression tag
Gly -3	-	expression tag
Ser -2	-	expression tag
Ser -1	-	expression tag
Gly 0	-	expression tag

v: 1 - 393 (UniProt: C4R997)

PDB	External Database	Details
Gly -2	-	expression tag
Ser -1	-	expression tag
Ala 0	-	expression tag

x: 1 - 365 (UniProt: C4R1E6)

PDB	External Database	Details
Met -29	-	initiating methionine
Lys -28	-	expression tag
Asp -27	-	expression tag
His -26	-	expression tag
Leu -25	-	expression tag
Ile -24	-	expression tag
His -23	-	expression tag
Asn -22	-	expression tag
His -21	-	expression tag
His -20	-	expression tag
Lys -19	-	expression tag
His -18	-	expression tag
Glu -17	-	expression tag
His -16	-	expression tag
Ala -15	-	expression tag
His -14	-	expression tag
Ala -13	-	expression tag
Glu -12	-	expression tag
His -11	-	expression tag
Leu -10	-	expression tag
Tyr -9	-	expression tag
Phe -8	-	expression tag
Gln -7	-	expression tag
Gly -6	-	expression tag
Ser -5	-	expression tag
Ser -4	-	expression tag
Gly -3	-	expression tag
Ser -2	-	expression tag
Ser -1	-	expression tag
Gly 0	-	expression tag

Sequence viewer

Contents of the asymmetric unit

Polymers	Number of chains	33
Polymers	Total formula weight	1427406.2
Non-Polymers*	Number of molecules	11
Non-Polymers*	Total formula weight	678.4
All*	Total formula weight	1428084.6

*Water molecules are not included.

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		Validation report (PDF)